An Introduction to Evolution

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An Introduction to Evolution

• Dr. Chrisantha Fernando
• Systems Biology Centre
• University of Birmingham

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What does Evolution explain?

• To explain how different animals and plants have
  become adapted to different environmental
  conditions over many generations.
• Evolution is the process by which living things
  become adapted to their environment over many
  generations.

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What is Evolution?

• Evolution occurs in populations of agents some of
  which produce offspring. The 'fitter' ones tend
  to produce more.
• Over many generations, the make-up of the
  population changes without the need for any
  individual to change. Over successive
  generations, the 'species' changes, in some sense
  adapts to the conditions.

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The Horse
Open country, ran from predators.
One toe
Muscles tend to be found at the upper part of the
leg, later on.
Lower part is less heavy.
Easier acceleration and deceleration -gt less
energy on galloping.
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Karl Sims Artificial Evolution

• Evolved virtual body plans in a simulated
  physical environment
• Used artificial evolution in the computer
• Show video.

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Evidence for Evolution

• Selective breeding for phenotypic traits, e.g.
  cows for milk, chickens for eggs, dogs for
  friendliness, mice for better teeth.
• Similarities between different species allows
  inference of an evolutionary tree.
• Moths in Birmingham during the Industrial
  Revolution.

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Breeding
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Homology
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Moths in Birmingham
1996
1956
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Evolution by Natural Selection

• Natural selection is an algorithm that works iff
• Multiplication. Entities should give rise to more
  entities of the same kind.
• Like begets like A type entities produce A type
  entities, B type entities produce B type
  entities, and so on.
• Variability. Heredity is not exact occasionally
  A type objects give rise to A' type objects.
  Undirected.
• Entities of different types have a hereditary
  difference in their survival. Directed.

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Natural Selection of Paper Gliders

• 1.Generate 20 random sequences of folding
  instructions
• 2.Fold each piece of paper according to
  instructions written on them.
• 3.Throw them all out of the window
• 4.Pick up the ones that went furthest, look at
  the instrns.
• 5.Produce 20 new pieces of paper, writing on each
  bits of sequences from parent pieces of paper.
• 6.Repeat from (2) on.
• This is Inman Harveys example.

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Fold TL to BR towards you Fold horiz middle
away Fold vertical middle towards
Fold TR to BL towards you Fold horiz middle
away Fold vertical middle away
I. Harvey.
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Evolving Tables Hornby et al
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Natural Selection in the Lab

• Sol Spiegelmans experiment with Q-beta replicase
  enzyme.

R
R
R
RNA
RNA
RNA
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Serial Dilution, like with homeopathy
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Natural Selection in the CPU

• Tierra (Tom Ray) and Avida.

Parasites Yellow
Immune Hosts
Red Starting Set
Organisms compete for CPU time to replicate.
A reaper randomly removes organisms.
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An example Tierran Organism
nop_1 01 47 copy loop template COPY
LOOP OF 80AAA nop_0 00 48 copy loop
template nop_1 01 49 copy loop
template nop_0 00 50 copy loop
template mov_iab 1a 51 move contents of bx
to ax (copy instruction) dec_c 0a 52
decrement cx if_cz 05 53 if cx 0 perform
next instruction, otherwise skip it jmp 14
54 jump to template below (copy procedure
exit) nop_0 00 55 copy procedure exit
compliment nop_1 01 56 copy procedure exit
compliment nop_0 00 57 copy procedure exit
compliment nop_0 00 58 copy procedure exit
compliment inc_a 08 59 increment ax (point
to next instruction of daughter) inc_b 09
60 increment bx (point to next instruction of
mother) jmp 14 61 jump to template below
(copy loop) nop_0 00 62 copy loop
compliment nop_1 01 63 copy loop
compliment nop_0 00 64 copy loop
compliment nop_1 01 65 copy loop compliment
(10 instructions executed per loop)
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Evolutionary Dynamics in Tierra.

• Smaller self-replicating mutants require less CPU
  time (energy/resource), so replicate faster.
• Parasites appeared 45 instructions long, able to
  use the code of their neighbors.
• Hyperparasites appear that are even smaller and
  faster at replicating.

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Natural Selection as movement over a fitness
landscape.
F
Random
Smooth
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Neutrality.
Constant innovation -- You never get stuck !
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Examples of Neutrality of GP Map.

• RNA Sequence --gt RNA Structure.
• Evolvable Hardware.

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William Paley and the Eye

• People said evolution could not produce the eye
  by small improvements, but it can.
• Computer experiments helped confirm this.
• To suppose that the eye could have been formed
  by natural selection, seems, I freely confess,
  absurd in the highest possible degree, (Darwin,
  The Origin of Species).

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Nilssons Computer Simulation
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The New Eye
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The Origin of Life

• Chicken and Eggs, Catch 22s and the Oroboros.
• How did natural selection start without genes
  that could undergo natural selection in the first
  place?
• How did the molecules that made genes come about
  in the first place?

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What was the first Self-Replicating Thing?
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The Major Transitions in Evolution (JMS ES 1995)

• 1. Replicating molecules to Populations of
  molecules in compartments
• 2. Independent replicators (probably
  RNA) to Chromosomes
• 3. RNA as both genes and enzymes to DNA as genes,
  proteins as enzymes
• Prokaryotes to Eukaryotes
• 5. Asexual clones to sexual populations
  evolution of sex
• 6. Protists to multicellular organisms animals,
  plants fungi evolution of multicellularity
• 7. Solitary individuals to colonies with
  non-reproductive castes
• 8. Primate societies to Human societies with
  language, enabling memes

Ammalgamation e.g. Chromosomes, eukaryotes,
sex multicellular colonies. Specialization e.g.
DNA protein, organelles, anisogamy, tissues,
castes Obligate Symbiosis e.g. Organelles,
tissues, castes Conflict Mediation Meiotic
drive (selfish non-Mendelian genes),
parthenogenesis, cancers, coup détat New
Information Transmission Techniques. DNA-protein,
cell heredity, epigenesis, universal grammar.
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What is Life? (Tibor Ganti,1971)

• If you went to Mars and found a pink fluffy
  object, how would you work out if it was alive?
• Boundary
• Metabolism
• Informational Control System
• E.g. single cell, multi-cellular organism. Is a
  country alive?

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Problems in Evolution.

• How could sex evolve? Why only two sexes not
  three or four?
• How do new species come about?
• How does the genotype-phenotype map evolve, i.e.
  the evolution of evolvability.
• Can there be selection of groups or ecosystems in
  the wild? Chicken coops.

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Thanks to

• Inman Harvey
• Jon Rowe
• All sources used for Images from the Internet.
• QUESTIONS AND DISCUSSION if you like.